The expression of virulence factors in the bacterium Bordetella pertussis is regulated in an environmentally responsive fashion under the control of the two-component system encoded by the bvgAS locus. In recent years we have focused research efforts on understanding the mechanisms of gene regulation in this important human pathogen - specifically focussing on the genes encoding pertussis toxin (ptx) and filamentous hemagglutinin (fha). Within the past year we have performed a detailed genetic and biochemical analysis of two regions of the fha promoter, the high affinity primary binding site, and the lower affinity secondary binding region. The primary binding site analysis has helped us to define critical bases involved in DNA recognition and binding by BvgA, and to begin to predict the presence of binding sites in unknown sequences. The secondary binding region analysis revealed that there are no critical bases for BvgA interaction and binding in the context of cooperative interactions with BvgA bound to the primary site. DNA sequence analysis of a large number of random substitutions within either of these regions which were able to restore promoter activity has extended and confirmed these predictions. Together these results have increased our understanding of the mechanisms of virulence gene activation in this important human pathogen, and have continued to suggest ways that production of vaccine antigens may be increased.